Fig. 5

Genome-wide analysis of alternative splicing (AS) in both cotton genotypes under control and salt stress conditions. a The different types of AS, including IR, A5SS, A3SS and ES, are schematically illustrated. Exons are represented by boxes; introns, by lines. b The counts of each type of AS event in the control and after 4 h and 24 h of salt treatment of both cotton genotypes are shown. Comparison of functional categorization after 4 h (c) and 24 h (d) of salt stress revealed AS-DEGs between the E7 and NH genotypes. e Validation of the AS of selected genes detected by mRNA-seq via RT-PCR. The representative AS events (IR) in four stress-responsive genes were validated by RT-PCR and visualized using IGV browser. In the RT-PCR validation, the asterisk (*) on the right side denotes the AS form. In the IGV visualization, the exon–intron structure of each gene is given at the bottom of each panel. The grey peaks above the exon–intron structure indicate the RNA-seq read density across the gene, and the black arrows represent AS sites